Bioinformatics analysis of hub genes as osteoarthritis prognostic biomarkers.

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Therefore, the objective of this study was to identify and analyze the hub genes of OA combining with comprehensive bioinformatics analysis tools to provide theoretical basis in further OA effective therapies. Two sample sets of GSE46750 contained 12 pairs OA synovial membrane and normal samples harvested from patients as well as GSE98918 including 12 OA and non-OA patients were downloaded from the Gene Expression Omnibus database (GEO) database. Differentially expressed genes (DEGs) were identified using Gene Expression Omnibus 2R (GEO2R), followed by functional enrichment analysis, protein-protein interaction networks construction. The hub genes were identified and evaluated. An OA rat model was constructed, hematoxylin and eosin staining, safranin O/fast green staining, cytokines concentrations of serum were used to verify the model. The hub genes expression level in the knee OA samples were verified using RT-qPCR. The top 20 significantly up-regulated and down-regulated DEGs were screened out from the two datasets, respectively. The top 18 GO terms and 10 KEGG pathways were enriched. Eight hub genes were identified, namely MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA and ITGB2. Among them, the hub genes were all up-regulated in in vivo OA rat model, compared with healthy controls. The eight hub genes identified (MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA and ITGB2) were shown to be associated with OA. These genes can serve as disease markers to discriminate OA patients from healthy controls.", "claims": [{"id": "claim-method", "statement": "The DEGs were finally determined using a Benjamini–Hochberg FDR (false discovery rate) multiple testing correction, and p value was analyzed to correct false-positive results, which p ≤ 0.05 and |log2FC| ≥ 1 was defined as the threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38129488", "locator": "sections[4] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "The DEGs were finally determined using a Benjamini–Hochberg FDR (false discovery rate) multiple testing correction, and p value was analyzed to correct false-positive results, which p ≤ 0.05 and |log2FC| ≥ 1 was defined as the threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data in this study are available by contacting corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38129488", "locator": "sections[28] \"notes\" paragraph 1", "quote": "All data in this study are available by contacting corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Eight OA-associated hub genes were identified: MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA, and ITGB2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38129488", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Eight hub genes were identified, namely MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA and ITGB2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Eight OA-associated hub genes were identified: MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA, and ITGB2.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38129488"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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